WGBS Data Analysis Related

Question

[shrinka.genetics]

Hello I am using MethylKit package on WGBS Data. I have sucessfully plotted coverage, correlation and PCA plots. Now in the step of annotation, this error is coming. I hope hg 19 bed file is already inbuilt there in the package. Anybody can help me please regarding this error? any clue?

gene.obj<-read.transcript.features("subset.refseq.hg19.bed.txt") *Error in read.transcript.features("subset.refseq.hg19.bed.txt") : unused argument ("subset.refseq.hg19.bed.txt")*

Thanks Shrinka

[Papyrus]

It is possible that in your MethylKit version this function is deprecated. You can try running the empty function read.transcript.features() and see its output. As you can see in the vignette you would have to use genomation::readTranscriptFeatures

[shrinka.genetics]

Thanks. I installed genomation and then ran again, but now showing this error? any clue? Reading the table...

Error in file(filename, open = "r") : cannot open the connection In addition: Warning message: In file(filename, open = "r") : cannot open file 'subset.refseq.hg19.bed.txt': No such file or directory

[Papyrus]

The function is not finding your file. Are you in the correct location (working directory) or is the name of the file correctly spelled? Always post your function call in addition to the output being returned.

[shrinka.genetics]

My question is what do you mean by file? When I created myobj all of my files were in one directory and I am working under that directory. According to my understanding this ref annotation file is in built in the package. Whenever I am calling the library, it is expected that those are accessible. Is it correct or not?

gene.obj<-read.transcript.features("subset.refseq.hg19.bed.txt")

[shrinka.genetics]

Sorry, I get your point. I did that, by using getwd() command. [1] "C:/Users/SHRINKA SEN/Documents/R/win-library/3.6/methylKit/extdata"

now readtranscript command ran, but I am facing difficulty in annotation step Reading the table...

Calculating intron coordinates...

Calculating exon coordinates...

Calculating TSS coordinates...

Calculating promoter coordinates...

Outputting the final GRangesList...

Error in annotate.WithGenicParts(myDiff25p, gene.obj) : unused arguments (myDiff25p, gene.obj)

I ran empty argument to figure out things and changed it, but till I got that below mentioned error? any clue, how to solve it? Use functions in genomation package from Bioconductor Warning message: 'annotate.WithGenicParts' is deprecated. Use 'genomation::annotateWithGeneParts' instead. See help("Deprecated")

Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘annotateWithGeneParts’ for signature ‘"methylDiff", "CompressedGRangesList"’

[Papyrus]

As I stated before, I suggest you follow the vignette and the manual. If you use genomation::annotateWithGeneParts you will see in the manual that its input is a GRanges object. Are you using the as() function inside the annotateWithGenePartscall? This is clearly stated in the vignette: genomation::annotateWithGeneParts(as(myDiff25p,"GRanges"),gene.obj) (untested). Again, I ask you to write all of your code, not just the error messages, because I cannot know if you're writing the function call correctly.

[shrinka.genetics]

If I use old command after installing genomation, the same error is showing Error in read.transcript.features("subset.refseq.hg19.bed.txt") : unused argument ("subset.refseq.hg19.bed.txt")

I used the new command as I got the suggestion after running empty function Use functions in genomation package from Bioconductor See vignette for examples. Warning message: 'read.transcript.features' is deprecated. Use 'genomation::readTranscriptFeatures' instead. See help("Deprecated")